GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCalpha in Crocosphaera subtropica ATCC 51142

Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate WP_009546784.1 CCE_RS01385 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha

Query= BRENDA::A0A222AKA3
         (368 letters)



>NCBI__GCF_000017845.1:WP_009546784.1
          Length = 343

 Score =  154 bits (390), Expect = 3e-42
 Identities = 106/326 (32%), Positives = 161/326 (49%), Gaps = 33/326 (10%)

Query: 43  LLMYRAMVVGRAFNRQATAFSRQGRLAVYPSS-RGQEACQVGSALAVRPT-DWLFPTYRE 100
           L++Y  M +GR F  +      +GR+  +     GQEA   G   A+RP  D++  TYR+
Sbjct: 23  LMLYEDMTLGRLFEDKCAEMYYRGRMFGFVHLYNGQEAVSTGIIKALRPDEDYVSSTYRD 82

Query: 101 SVALLTRGIDPVQVLT-LFRGDQHC-------------------GYDPVTEHTAPQCTPL 140
            V  L+ G+ P +V+  LF  +  C                   GY  V E   P  T  
Sbjct: 83  HVHALSCGVPPREVMAELFGKETGCSKGRGGSMHLFSEKHRLLGGYAFVAEGI-PVATGA 141

Query: 141 ATQCLHAAGLADAARMAGDPI---VALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQN 197
           A Q  +         M GD     V + + GDGA++ G F E LN AA+ + P++++V+N
Sbjct: 142 AFQSKYRR------EMMGDETADQVTVCFFGDGASNNGQFFECLNMAALWKLPIIYVVEN 195

Query: 198 NQYAISVPLAKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLI 257
           N++AI +   + T+   +  KA+ + M GV +DG DVL V +   +A  RARAG GPTLI
Sbjct: 196 NKWAIGMAHNRATSQPEIYKKASVFDMVGVEVDGMDVLAVRKVAQEAIARARAGEGPTLI 255

Query: 258 EAVTYRIDAHTNADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAAD 317
           EA+TYR   H+ AD D   R   E   W ++DP+ RLE  L+   + +++  D I     
Sbjct: 256 EALTYRFRGHSLADPD-ELRSPDEKQFWGSKDPIQRLEAYLIEHNLANQSELDEIKQKVQ 314

Query: 318 AFAGELSARFSAPPTGDPMQMFRHVY 343
           A   +        P  DP +++R+V+
Sbjct: 315 ASVDDAVKFAEESPEPDPKELYRYVF 340


Lambda     K      H
   0.319    0.132    0.395 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 231
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 368
Length of database: 343
Length adjustment: 29
Effective length of query: 339
Effective length of database: 314
Effective search space:   106446
Effective search space used:   106446
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory